The primary goal of this project will be to monitor global gene expression patterns in response to Infectious hypodermal and hematopoietic necrosis virus (IHHNV) infection in Penaeus stylirostris. Changes in gene expression patterns have profound effects on biological functions. Natural processes within living organisms are coordinated by variations in many genes and their products (RNA and proteins) and are at the core of altered pathologic responses. Increasingly, focused researched efforts are emerging to understand invertebrate defense systems and host response to pathogens. The innate immune strategies developed within invertebrate systems serve as models for understanding host defense strategies in response to viral pathogens for both vertebrate and invertebrates. Currently, there are only two published reports in penaeids using expression analysis to discover genes involved in the immune system. These studies demonstrated increased regulation of previously identified defense peptides using the expressed sequence tag (EST) method. While useful, ESTs are more limited in their scope in that they do not generate comprehensive gene expression profiles. There are two techniques available for global gene expression analysis, cDNA microarray and serial analysis of gene expression (SAGE). Both are aimed at monitoring thousands of genes within a biological system under different experimental conditions, however, SAGE is the only technique that does not require prior knowledge of the genome of interest. In addition, SAGE analysis is based on the direct numerical counting of gene tags for comparison between libraries, rather than the arduous statistical methods required for microarray fluorophore signal intensity analysis. With this in mind, the objectives of this research are to compare global gene expression profiles between virally infected and healthy shrimp using SAGE. This will involve the creation of two SAGE libraries and sequencing approximately 400 clones, representing 16,000 different gene tags, from each library. The fulfillment of these objectives represents a unique opportunity to understand the invertebrate immune system as it relates to viral pathogenesis and will serve as a model to understand other animal, vertebrate and invertebrate, defense mechanisms.